This submission is in response to Notice Number NOT-OD-09-058 entitled: NIH Announces the Availability of Recovery Act Funds for Competitive Revision Applications. The development of massive parallel sequencing platforms opens new avenues of discovery that could significantly expand the scope of our work. We plan to develop a method for mapping paused Pol II across the entire Drosophila genome by combining permanganate genomic footprinting, chromatin immunoprecipitation, and massive parallel sequencing. Several recent studies have shown that Pol II is concentrated in the promoter proximal region of many genes and raise the possibility that this is a prominent regulatory step in gene expression. However, most studies have relied on chromatin immunoprecipitation, which is unable to determine if Pol II is transcriptionally engaged. Our method will provide a high resolution measure of the distribution of paused Pol II. We also want to combine ChIP and massive parallel sequencing to determine the distribution of a novel sequence specific DNA binding protein that our evidence indicates could be involved in promoter proximal pausing on 30% of the genes we predict have paused Pol II. PUBLIC HEALTH RELEVANCE: Control of gene expression is essential for normal development, and many diseases can be attributed to the miss-regulation of genes. Gene expression is usually controlled at the level of transcription. This research investigates mechanisms of transcriptional control using Drosophila as a model system for understanding the process in humans because Drosophila is amenable to genetic, molecular genetic and biochemical analyses.